Cleaned up Processor doc and exports.

modules/conop/doc/connectivity.rst

@@ -40,76 +40,112 @@ Processors
 --------------------------------------------------------------------------------
 
 The exact behaviour for a processor is implementation-specific. So far, two
-classes implement the processor interface: A heuristic and a rule-based processor. 
-The processor mainly differ in the source of their connectivity information. The
-Heuristicprocessor uses a hard-coded heuristic connectivity table for the 20 
-standard amino acids as well as nucleotides.For other compounds such as ligands
-the HeuristicProcessor runs a distance-based connectivity algorithm that connects
-two atoms if they are closer than a  certain threshold. The RuleBasedProcessor
-uses a connectivity library containing  all molecular components present in the
-PDB files on PDB.org. The library can  easily be extended with custom 
-connectivity information, if required. If a :doc:`compound library <compoundlib>` is 
-present, the :class:`RuleBasedProcessor` is enabled by default, otherwise the 
+classes implement the processor interface: A heuristic and a rule-based
+processor. The processor mainly differ in the source of their connectivity
+information. The Heuristicprocessor uses a hard-coded heuristic connectivity
+table for the 20  standard amino acids as well as nucleotides.For other
+compounds such as ligands the HeuristicProcessor runs a distance-based
+connectivity algorithm that connects two atoms if they are closer than a certain
+threshold. The RuleBasedProcessor uses a connectivity library containing all
+molecular components present in the PDB files on PDB.org. The library can easily
+be extended with custom  connectivity information, if required. If a
+:doc:`compound library <compoundlib>` is present, the
+:class:`RuleBasedProcessor` is enabled by default, otherwise the
 :class:`HeuristicProcessor` is used as a fallback.
 
 
-The Processor base class
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. class:: Processor
 
-  .. attribute:: connect
+  .. attribute:: check_bond_feasibility
 
-    Whether to connect atoms by bonds. Enabled by default. This also sets the
-    :attr:`~ost.mol.ResidueHandle.is_protein` property of residues when peptide
-    bonds are created. Turn this off if you would like to speed up the loading
-    process and do not require connectivity information to be present in your
-    structures.
+    Whether an additional bond feasibility check is performed. Disabled by
+    default. If turned on, atoms are only connected by bonds if they are within
+    a reasonable distance (as defined by :func:`IsBondFeasible`).
 
     :type: :class:`bool`
 
-  .. attribute:: zero_occ_treatment
+  .. attribute:: assign_torsions
 
-    Controls the behaviour of importing atoms with zero occupancy. By default, this 
-    is set to silent.
+    Whether backbone torsions should be added to the backbone. Enabled by
+    default. If turned on, PHI, PSI and OMEGA torsions are assigned to the
+    peptide residues. See also :func:`AssignBackboneTorsions`.
 
-    :type: :class:`str`
+    :type: :class:`bool`
 
-  .. attribute:: check_bond_feasibility
+  .. attribute:: connect
 
-    Whether an additional bond feasibility check is performed. Disabled by default.
-    Turn this on, if you would like to connect atoms by bonds only if they are 
-    within a reasonable distance.
-    See also :func:`IsBondFeasible`.
+    Whether to connect atoms by bonds. Enabled by default. Turn this off if you
+    would like to speed up the loading process and do not require connectivity
+    information to be present in your structures. Note though that
+    :attr:`peptide_bonds` may be ignored if this is turned off.
 
     :type: :class:`bool`
 
-  .. attribute:: assign_torsions
+  .. attribute:: peptide_bonds
 
-    Whether backbone torsions should be added to the backbone. Disabled by default.
-    Set to true, to assign PHI, PSI and OMEGA torsions to the peptide residues.
-    See also :func:`AssignBackboneTorsions`.
+    Whether to connect residues by peptide bonds. Enabled by default. This also
+    sets the :attr:`~ost.mol.ResidueHandle.is_protein` property of residues when
+    peptide bonds are created. Turn this off if you would like to create your
+    own peptide bonds.
 
     :type: :class:`bool`
 
+  .. attribute:: zero_occ_treatment
+
+    Controls the behaviour of importing atoms with zero occupancy. By default,
+    this is set to warn.
+
+    :type: :class:`ConopAction`
 
   .. method:: Process(ent)
   
     Processess the entity *ent* according to the current options.
 
 
-The RuleBasedProcessor class
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. class:: HeuristicProcessor(check_bond_feasibility=False, \
+                              assign_torsions=True, connect=True, \
+                              peptide_bonds=True, zero_occ_treatment=CONOP_WARN)
+   
+  The :class:`HeuristicProcessor` implements the :class:`Processor` interface.
+  Refer to its documentation for methods and accessors common to all processor.
+
+  :param check_bond_feasibility: Sets :attr:`~Processor.check_bond_feasibility`
+  :param assign_torsions: Sets :attr:`~Processor.assign_torsions`
+  :param connect: Sets :attr:`~Processor.connect`
+  :param peptide_bonds: Sets :attr:`~Processor.peptide_bonds`
+  :param zero_occ_treatment: Sets :attr:`~Processor.zero_occ_treatment`
+
+
+.. class:: RuleBasedProcessor(compound_lib, fix_elements=True, \
+                              strict_hydrogens=False, \
+                              unknown_res_treatment=CONOP_WARN, \
+                              unknown_atom_treatment=CONOP_WARN, \
+                              check_bond_feasibility=False, \
+                              assign_torsions=True, connect=True, \
+                              peptide_bonds=True, zero_occ_treatment=CONOP_WARN)
+   
+  The :class:`RuleBasedProcessor` implements the :class:`Processor` interface.
+  Refer to its documentation for methods and accessors common to all processor.
+
+  :param compound_lib: The compound library to use
+  :type compound_lib:  :class:`CompoundLib`
+  :param fix_elements: Sets :attr:`fix_elements`
+  :param strict_hydrogens: Sets :attr:`strict_hydrogens`
+  :param unknown_res_treatment: Sets :attr:`unk_atom_treatment`
+  :param unknown_atom_treatment: Sets :attr:`unk_res_treatment`
+  :param check_bond_feasibility: Sets :attr:`~Processor.check_bond_feasibility`
+  :param assign_torsions: Sets :attr:`~Processor.assign_torsions`
+  :param connect: Sets :attr:`~Processor.connect`
+  :param peptide_bonds: Sets :attr:`~Processor.peptide_bonds`
+  :param zero_occ_treatment: Sets :attr:`~Processor.zero_occ_treatment`
 
-.. class:: RuleBasedProcessor(compound_lib)
+  .. attribute:: fix_elements
 
-   :param compound_lib: The compound library
-   :type compound_lib: :class:`CompoundLib`
-   
-   The :class:`RuleBasedProcessor` implements the :class:`Processor` interface.
-   Refer to its documentation for methods and accessors common to all processor.
+    Whether the element of the atom should be changed to the atom defined in the
+    compound library. Enabled by default.
+
+    :type: :class:`bool`
 
-   
   .. attribute:: strict_hydrogens
 
     Whether to use strict hydrogen naming rules outlined in the compound library.
@@ -119,22 +155,21 @@ The RuleBasedProcessor class
 
   .. attribute:: unk_atom_treatment
 
-    Treatment upon encountering an unknown atom. Default: 'warn'.
-
+    Treatment upon encountering an unknown atom. Warn by default.
 
-    :type: :class:`str`
+    :type: :class:`ConopAction`
 
   .. attribute:: unk_res_treatment
 
-    Treatment upon encountering an unknown residue
-
-    :type: :class:`str`
+    Treatment upon encountering an unknown residue. Warn by default.
 
-  .. attribute:: fix_elements
+    :type: :class:`ConopAction`
 
-    Whether the element of the atom should be changed to the atom defined in the 
-    compound library. Enabled by default.
 
-    :type: :class:`bool`
+.. class:: ConopAction
 
+  Defines actions to take when certain events happen during processing. Possible
+  values:
 
+    ``CONOP_WARN``, ``CONOP_SILENT``, ``CONOP_REMOVE``, ``CONOP_REMOVE_ATOM``,
+    ``CONOP_REMOVE_RESIDUE``, ``CONOP_FATAL``

modules/conop/pymod/export_processor.cc

@@ -80,10 +80,14 @@ void export_processor() {
     .add_property("check_bond_feasibility", 
                   &Processor::GetCheckBondFeasibility,
                   &Processor::SetCheckBondFeasibility)
-    .add_property("connect", &Processor::GetConnect,
-                 &Processor::SetConnect)
     .add_property("assign_torsions", &Processor::GetAssignTorsions,
-                 &Processor::SetAssignTorsions)
+                  &Processor::SetAssignTorsions)
+    .add_property("connect", &Processor::GetConnect,
+                  &Processor::SetConnect)
+    .add_property("peptide_bonds", &Processor::GetConnectAminoAcids,
+                  &Processor::SetConnectAminoAcids)
+    .add_property("zero_occ_treatment", &Processor::GetZeroOccTreatment,
+                  &Processor::SetZeroOccTreatment)
     .def("Process", &Processor::Process, 
          (arg("ent"), arg("log_diags")=true))
   ;